Obesity, diabetes and metabolic disorders represent hugely significant problems concerning the health in Western countries and the study of gut microbiota in metabolic pathologies is part of this framework. Diet effects on intestinal microbial composition and its role in pathogenetic mechanisms responsible for both obesity and systemic, hepatic and adipose tissue inflammation, represent at the moment one of this mostpromising topic in gastroenterology research. Gut health safety is essential, but it needs to be further explored in order to understand and interrupt the pathogenetic mechanisms, which support a large number of diseases. The aim of this review is to describe what are the modifications of gut microbial composition that occur in metabolic disorders and the role of gut microbiota in the pathogenesis of several diseases such as obesity, metabolic syndrome and type II diabetes mellitus, showing how gut microbiota and adipose tissue, liver and brain, together with intestinal permeability increase, carry out an interconnection systemthat plays a pivotal role in the field.